Added chado_linker_phenotype and chado_linker_genotype fields

tripal_chado/includes/fields/chado_linker__genotype.inc

@@ -0,0 +1,217 @@
+<?php
+
+class chado_linker__genotype extends TripalField {
+
+  /**
+   * @see TripalField::field_info()
+   */
+  public function field_info() {
+    return array(
+      'label' => t('Genotypes'),
+      'description' => t('Associates an indviddual or organization with
+          this record.'),
+      'default_widget' => 'chado_linker__genotype_widget',
+      'default_formatter' => 'chado_linker__genotype_formatter',
+      'settings' => array(),
+      'storage' => array(
+        'type' => 'field_chado_storage',
+        'module' => 'tripal_chado',
+        'active' => TRUE
+      ),
+    );
+  }
+  /**
+   * @see TripalField::widget_info()
+   */
+  function widget_info() {
+    return array(
+      'label' => t('Genotypes'),
+      'field types' => array('chado_linker__genotype'),
+    );
+  }
+
+  /**
+   * @see TripalField::formatter_info()
+   */
+  public function formatter_info() {
+    return array(
+      'label' => t('Genotypes'),
+      'field types' => array('chado_linker__genotype'),
+      'settings' => array(
+      ),
+    );
+  }
+  /**
+   * @see TripalField::attach_info()
+   */
+  public function attach_info($entity_type, $bundle, $settings) {
+    $field_info = array();
+
+    $table_name = $settings['data_table'];
+    $type_table = $settings['type_table'];
+    $type_field = $settings['field'];
+    $cv_id      = $settings['cv_id'];
+    $cvterm_id  = $settings['cvterm_id'];
+
+    // If the linker table does not exists then we don't want to add attach.
+    $genotype_table = $table_name . '_genotype';
+    if (!chado_table_exists($genotype_table)) {
+      return $field_info;
+    }
+
+    $schema = chado_get_schema($genotype_table);
+    $pkey = $schema['primary key'][0];
+
+    // Initialize the field array.
+    $field_info = array(
+      'field_name' => $table_name . '__genotype',
+      'field_type' => 'chado_linker__genotype',
+      'widget_type' => 'chado_linker__genotype_widget',
+      'widget_settings' => array('display_label' => 1),
+      'description' => '',
+      'label' => 'Genotypes',
+      'is_required' => 0,
+      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
+      'storage' => 'field_chado_storage',
+      'field_settings' => array(
+        'chado_table' => $genotype_table,
+        'chado_column' => $pkey,
+        'base_table' => $table_name,
+        'semantic_web' => array(
+          'name' => 'genotype',
+          'accession' => 'genotype',
+          'ns' => 'local',
+          'nsurl' => '',
+        ),
+      ),
+    );
+    return $field_info;
+  }
+
+  /**
+   * @see TripalField::formatter_view()
+   */
+  public function formatter_view(&$element, $entity_type, $entity,
+      $field, $instance, $langcode, $items, $display) {
+        // Get the settings
+        $settings = $display['settings'];
+        $record = $entity->chado_record;
+
+        $headers = array('Name', 'Description', 'Type');
+        $rows = array();
+dpm($items);
+        foreach ($items as $delta => $item) {
+          $genotype = $item['value'];
+          if (!$genotype) {
+            continue;
+          }
+
+          // Get the field values
+          $genotype_name = $genotype['name'];
+          $description = $genotype['description'];
+          $type = $genotype['type'];
+
+          // Add a link i there is an entity.
+          if (array_key_exists('entity_id', $item) and $item['entity_id']) {
+            $entity_id = $item['entity_id'];
+            $genotype_name = l($genotype_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
+          }
+          $rows[] = array($genotype_name, $description, $type);
+        }
+        $table = array(
+          'header' => $headers,
+          'rows' => $rows,
+          'attributes' => array(
+            'id' => 'tripal_linker-table-genotype-object',
+            'class' => 'tripal-data-table'
+          ),
+          'sticky' => FALSE,
+          'caption' => "",
+          'colgroups' => array(),
+          'empty' => 'No genotypes available',
+        );
+        $content = theme_table($table);
+
+        // once we have our table array structure defined, we call Drupal's theme_table()
+        // function to generate the table.
+        $element[$delta] = array(
+          '#type' => 'markup',
+          '#markup' => $content,
+        );
+  }
+
+
+  /**
+   * @see TripalField::widget_form()
+   */
+  public function widget_form(&$widget, $form, $form_state, $field, $instance,
+      $langcode, $items, $delta, $element) {
+
+  }
+
+  /**
+   * @see TripalField::load()
+   */
+  public function load($field, $entity, $details) {
+    $record = $details['record'];
+    $field_name = $field['field_name'];
+    $field_type = $field['type'];
+    $field_table = $field['settings']['chado_table'];
+    $field_column = $field['settings']['chado_column'];
+
+    // Get the FK that links to the base record.
+    $schema = chado_get_schema($field_table);
+    $base_table = $details['record']->tablename;
+    $pkey = $schema['primary key'][0];dpm($schema);
+    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
+    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
+
+
+    // Set some defaults for the empty record.
+    $entity->{$field_name}['und'][0] = array(
+      'value' => array(),
+      $field_table . '__' . $pkey => '',
+      $field_table . '__' . $fkey_lcolumn => '',
+      $field_table . '__' . 'genotype_id' => '',
+      // Ignore the synonym_sgml column for now.
+    );
+
+    $linker_table = $base_table . '_genotype';
+    $options = array(
+      'return_array' => 1,
+      'include_fk' => array(
+        'genotype_id' => array(
+          'type_id' => array(
+            'dbxref_id' => array(
+              'db_id' => TRUE,
+            ),
+          ),
+        ),
+        $fkey_lcolumn => TRUE,
+      ),
+    );
+    $record = chado_expand_var($record, 'table', $linker_table, $options);
+    $genotype_linkers = $record->$linker_table;
+    if ($genotype_linkers) {
+      foreach ($genotype_linkers as $i => $genotype_linker) {
+        $genotype = $genotype_linker->genotype_id;
+        $entity->{$field_name}['und'][$i] = array(
+          'value' => array(
+            '@type' => $genotype->type_id->dbxref_id->db_id->name . ':' . $genotype->type_id->dbxref_id->accession,
+            'type' => $genotype->type_id->name,
+            'name' => $genotype->name,
+            'description' => $genotype->description,
+          ),
+          $field_table . '__' . $pkey => $genotype_linker->$pkey,
+          $field_table . '__' . $fkey_lcolumn => $genotype_linker->$fkey_lcolumn->$fkey_lcolumn,
+          $field_table . '__' . 'genotype_id' => $genotype->genotype_id
+        );
+
+        if ($genotype && property_exists($genotype, 'entity_id')) {
+          $entity->{$field_name}['und'][$i]['entity_id'] = $genotype->entity_id;
+          $entity->{$field_name}['und'][$i]['entity_type'] = 'TripalEntity';
+        }
+      }
+    }
+  }
+}

tripal_chado/includes/fields/chado_linker__phenotype.inc

@@ -0,0 +1,217 @@
+<?php
+
+class chado_linker__phenotype extends TripalField {
+
+  /**
+   * @see TripalField::field_info()
+   */
+  public function field_info() {
+    return array(
+      'label' => t('Genotypes'),
+      'description' => t('Associates an indviddual or organization with
+          this record.'),
+      'default_widget' => 'chado_linker__phenotype_widget',
+      'default_formatter' => 'chado_linker__phenotype_formatter',
+      'settings' => array(),
+      'storage' => array(
+        'type' => 'field_chado_storage',
+        'module' => 'tripal_chado',
+        'active' => TRUE
+      ),
+    );
+  }
+  /**
+   * @see TripalField::widget_info()
+   */
+  function widget_info() {
+    return array(
+      'label' => t('Genotypes'),
+      'field types' => array('chado_linker__phenotype'),
+    );
+  }
+
+  /**
+   * @see TripalField::formatter_info()
+   */
+  public function formatter_info() {
+    return array(
+      'label' => t('Genotypes'),
+      'field types' => array('chado_linker__phenotype'),
+      'settings' => array(
+      ),
+    );
+  }
+  /**
+   * @see TripalField::attach_info()
+   */
+  public function attach_info($entity_type, $bundle, $settings) {
+    $field_info = array();
+
+    $table_name = $settings['data_table'];
+    $type_table = $settings['type_table'];
+    $type_field = $settings['field'];
+    $cv_id      = $settings['cv_id'];
+    $cvterm_id  = $settings['cvterm_id'];
+
+    // If the linker table does not exists then we don't want to add attach.
+    $phenotype_table = $table_name . '_phenotype';
+    if (!chado_table_exists($phenotype_table)) {
+      return $field_info;
+    }
+
+    $schema = chado_get_schema($phenotype_table);
+    $pkey = $schema['primary key'][0];
+
+    // Initialize the field array.
+    $field_info = array(
+      'field_name' => $table_name . '__phenotype',
+      'field_type' => 'chado_linker__phenotype',
+      'widget_type' => 'chado_linker__phenotype_widget',
+      'widget_settings' => array('display_label' => 1),
+      'description' => '',
+      'label' => 'Genotypes',
+      'is_required' => 0,
+      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
+      'storage' => 'field_chado_storage',
+      'field_settings' => array(
+        'chado_table' => $phenotype_table,
+        'chado_column' => $pkey,
+        'base_table' => $table_name,
+        'semantic_web' => array(
+          'name' => 'phenotype',
+          'accession' => 'phenotype',
+          'ns' => 'local',
+          'nsurl' => '',
+        ),
+      ),
+    );
+    return $field_info;
+  }
+
+  /**
+   * @see TripalField::formatter_view()
+   */
+  public function formatter_view(&$element, $entity_type, $entity,
+      $field, $instance, $langcode, $items, $display) {
+        // Get the settings
+        $settings = $display['settings'];
+        $record = $entity->chado_record;
+
+        $headers = array('Name', 'Value', 'Type');
+        $rows = array();
+
+        foreach ($items as $delta => $item) {
+          $phenotype = $item['value'];
+          if (!$phenotype) {
+            continue;
+          }
+
+          // Get the field values
+          $phenotype_name = $phenotype['name'];
+          $value = $phenotype['value'];
+          $type = $phenotype['type'];
+
+          // Add a link i there is an entity.
+          if (array_key_exists('entity_id', $item) and $item['entity_id']) {
+            $entity_id = $item['entity_id'];
+            $phenotype_name = l($phenotype_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
+          }
+          $rows[] = array($phenotype_name, $value, $type);
+        }
+        $table = array(
+          'header' => $headers,
+          'rows' => $rows,
+          'attributes' => array(
+            'id' => 'tripal_linker-table-phenotype-object',
+            'class' => 'tripal-data-table'
+          ),
+          'sticky' => FALSE,
+          'caption' => "",
+          'colgroups' => array(),
+          'empty' => 'No phenotypes available',
+        );
+        $content = theme_table($table);
+
+        // once we have our table array structure defined, we call Drupal's theme_table()
+        // function to generate the table.
+        $element[$delta] = array(
+          '#type' => 'markup',
+          '#markup' => $content,
+        );
+  }
+
+
+  /**
+   * @see TripalField::widget_form()
+   */
+  public function widget_form(&$widget, $form, $form_state, $field, $instance,
+      $langcode, $items, $delta, $element) {
+
+  }
+
+  /**
+   * @see TripalField::load()
+   */
+  public function load($field, $entity, $details) {
+    $record = $details['record'];
+    $field_name = $field['field_name'];
+    $field_type = $field['type'];
+    $field_table = $field['settings']['chado_table'];
+    $field_column = $field['settings']['chado_column'];
+
+    // Get the FK that links to the base record.
+    $schema = chado_get_schema($field_table);
+    $base_table = $details['record']->tablename;
+    $pkey = $schema['primary key'][0];
+    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
+    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
+
+
+    // Set some defaults for the empty record.
+    $entity->{$field_name}['und'][0] = array(
+      'value' => array(),
+      $field_table . '__' . $pkey => '',
+      $field_table . '__' . $fkey_lcolumn => '',
+      $field_table . '__' . 'phenotype_id' => '',
+      // Ignore the synonym_sgml column for now.
+    );
+
+    $linker_table = $base_table . '_phenotype';
+    $options = array(
+      'return_array' => 1,
+      'include_fk' => array(
+        'phenotype_id' => array(
+          'attr_id' => array(
+            'dbxref_id' => array(
+              'db_id' => TRUE,
+            ),
+          ),
+        ),
+        $fkey_lcolumn => TRUE,
+      ),
+    );
+    $record = chado_expand_var($record, 'table', $linker_table, $options);
+    $phenotype_linkers = $record->$linker_table;
+    if ($phenotype_linkers) {
+      foreach ($phenotype_linkers as $i => $phenotype_linker) {
+        $phenotype = $phenotype_linker->phenotype_id;
+        $entity->{$field_name}['und'][$i] = array(
+          'value' => array(
+       '@type' => $phenotype->attr_id->dbxref_id->db_id->name . ':' . $phenotype->type_id->dbxref_id->accession,
+            'type' => $phenotype->attr_id->name,
+            'name' => $phenotype->name,
+            'value' => $phenotype->value,
+          ),
+          $field_table . '__' . $pkey => $phenotype_linker->$pkey,
+          $field_table . '__' . $fkey_lcolumn => $phenotype_linker->$fkey_lcolumn->$fkey_lcolumn,
+          $field_table . '__' . 'phenotype_id' => $phenotype->phenotype_id
+        );
+
+        if ($phenotype && property_exists($phenotype, 'entity_id')) {
+          $entity->{$field_name}['und'][$i]['entity_id'] = $phenotype->entity_id;
+          $entity->{$field_name}['und'][$i]['entity_type'] = 'TripalEntity';
+        }
+      }
+    }
+  }
+}